If I correctly recall the definitions, then
1. $\dim_FD=(\deg D)^2$ (this holds for all division algebras that are f.d. over their center).
2. $\dim_E A^E=\dim_F A$ (this is obvious).
3. If $D$ is a division algebra with center $F$, then $D\otimes_F E$ is a central simple algebra with center $E$. Therefore, by Wedderburn's Theorem, $$D\otimes_FE\simeq M_k(D_E)$$ for some division algebra $D_E$ with center $E$.
4. So $$k^2\dim_E D_E= \dim_E M_k(D_E)=\dim_E(D\otimes_FE)=\dim_F D.$$
5. Combining items 1 and 4 gives us $$(\deg D)^2=\dim_F D=k^2\dim_E D_E=k^2(\deg D_E)^2,$$ and consequently $$\deg D= k\cdot \deg D_E.$$
6. So $\deg D_E\mid \deg D$.
By your definition $\operatorname{Ind}(A)=\deg D$ and $\operatorname{Ind}(A^E)=\deg D_E$, so we are done.